The Justice Department has acknowledged errors and deficiencies in a controversial report issued a year ago that implied a link between terrorism in the United States and immigration, but — for the second and final time — officials have declined to retract or correct the document.

Released by the departments of Justice and Homeland Security, the report stated that 402 of 549 individuals — nearly 3 in 4 — convicted of international terrorism charges since the Sept. 11, 2001, terrorist attacks were foreign-born.

The report was written in compliance with President Trump’s March 2017 executive order halting immigration from six majority-Muslim countries.

Critics immediately expressed alarm at what they considered highly misleading data presented without context. They called it an attempt to misuse law enforcement agencies to advance a political agenda in opposition to immigration, and former senior counterterrorism officials warned it could play into terrorists’ hands by fueling misperceptions about radicalization and stoking societal divides.

Several government watchdog and civil liberty groups in May sued the two agencies in two federal courts, seeking a retraction or correction under the little-known Information Quality Act. The agencies refused, and the courts stayed the lawsuits to allow time for an administrative appeal.

Now, after two rounds, the Justice Department has told the groups it will not retract or correct the document. Rather, “in future reports, the department can strive to minimize the potential for misinterpretation,” Michael H. Allen, deputy assistant attorney general for policy, management and planning, wrote in a Dec. 21 letter to the groups.

It is, experts said, a rare admission from the department that its reporting may have confused and misled the public. “This is the government’s statement on the risk of terrorism presented by foreign-born individuals in the United States, and it’s critical that it be accurate — not just because the law requires it but because they have a duty to the American people to accurately report information of this type,” said Ben Berwick, counsel for Protect Democracy, one of the groups that sued the government and is representing the others in court.

Otherwise, he said, it “erodes trust in the government. It erodes democracy.”

One flaw the Justice Department acknowledged was the report’s assertion that between 2003 and 2009, immigrants were convicted of 69,929 sex offenses, which “in most instances constitutes gender-based violence against women.”

But, Allen said in his letter, “the alleged misrepresented data constitute mere editorial errors which the [law] does not obligate the agencies to withdraw or correct.”

Still, he added, “the department appreciates being made aware of such errors so they will not be repeated.”

Berwick said the errors were “not merely editorial.” The nearly 70,000 offenses spanned a period from 1955 to 2010 — 55 years, not six; the data covered arrests, not convictions; and one arrest could be for multiple offenses, he said, citing the Government Accountability Office, which provided the underlying data.

Critics also decried the report’s inclusion of eight “illustrative examples” of foreign-born individuals out of a pool of 402 convicted of international terrorism. Six of the eight cases involved people admitted to the country as family members of legal residents or U.S. citizens, which Protect Democracy contended was an effort to portray “chain migration” as a threat.

“On reconsideration, the department acknowledges that a focus on eight seemingly similar ‘illustrative examples’ from a list of more than 400 convictions could cause some readers of the report to question its objectivity,” Allen wrote.

At least 189 of the 549 peopleconvicted were caught up in an investigation with a link to international terrorism but not charged with an offense directly related to terrorism, Berwick said, citing Justice Department data. It is unclear how many were foreign-born. Nonetheless, that would change the statistics considerably, but the department did not address that in its letter.

The report included about 100 foreign-born individuals who were extradited to the United States to stand trial for terrorism-related crimes committed overseas, without clarifying the reason they were brought to the country, Berwick said. That is misleading because the report creates a false impression that those extradited came in as immigrants, he said.

“There is no requirement in either the [law or department guidelines] that agencies must always provide underlying data when disseminating information to the public,” Allen wrote.

The coalition of groups is considering whether to return to court.

Correction: An earlier version of this story misidentified the Government Accountability Office.